1. Introduction

  • This function is designed to provide insights into spatial and functional associations of CMRs (Chemical Modifications of RNAs). This function takes the CMRs in BED format and genome annotation in GTF (Gene Transfer Format) format as input, then the manner of distribution of CMRs in the genome and transcriptome is statistically analyzed and visualized, including the number of peaks in genomic feature (e.g. promoter, exon, intron, etc), the regions of enrichment of CMRs within transcripts, the enrichment of CMRs in transcriptional start/stop site and the enrichment of CMRs in splicing sites.

2. The number of peaks in each genomic feature

  • The following figure displays the number of input peaks overlaped with each genomic feature including Transcript, Exon, 3’UTR, CDS, Intron, Promoter, 5’UTR and Intergenic.

3. The number of peaks in each type of RNA

  • The following table shows the number of peaks overlapped (at least 1nt) with each type of RNA.
Gene type Count
protein_coding 11941
tRNA 2
lincRNA 69
snoRNA 0
snRNA 0
miRNA 0
pre_miRNA 0
sense_intronic 0
SRP_RNA 0
rRNA 0
ncRNA 0
antisense_RNA 0
RNase_MRP_RNA 0

4. The regions of enrichment of CMRs within transcripts

  • The following figure displays the enrichment of CMRs on meta-RNA, to be specific, each transcript are splited into bins of 30 nt, then the relative position of each bin for each feature (5’UTR, CDS and 3’UTR) is calculated. The CMRs enrichment can be obtained by overlap input peaks with each 30nt bin.
## [1] "total 138424 transcripts extracted ..."
## [1] "total 53527 transcripts left after ambiguity filter ..."
## [1] "total 17059 mRNAs left after component length filter ..."
## [1] "total 2118 ncRNAs left after ncRNA length filter ..."
## [1] "Building Guitar Coordinates. It may take a few minutes ..."
## [1] "Guitar Coordinates Built ..."

5. The enrichment of CMRs in transcriptional start/stop site

  • The figures below display the enrichment of CMRs in transcription start and end site, respectively. To be specific, the x axis represents the relative position of transcription start/end site, 0 indicates the meta-transcription start/end site, negative number and positive number represent the upstream and downstream of transcription start/end site, respectively.

6. The enrichment of CMRs in splicing sites

  • The figures below display the enrichment of CMRs in 3’ and 5’ end of exons, respectively. To be specific, the x axis represents the relative position of 3’ and 5’ end of exons, 0 indicates the 3’ and 5’ end of exons, negative number and positive number represent the upstream and downstream of 3’ and 5’ end of exons, respectively.